It sounds like your boot manager was installed onto your second hard drive.
The simple answer is to reconnect your 2nd hard drive, initiate a windows easy transfer to backup your settings, disconnect all other drives, re-install windows, reconnect all other drives and restore your settings. Note:- WET will not transfer all your settings.
The complicated answer is to shrink your OS partition by as much as you can, copy it using imaging software to another partition on a spare drive, disconnect all drives except the one you want to install your OS onto, re-install windows, reconnect your other drives and restore your backup partition to your OS drive. You may also have to change the boot ordr in your bios.